Advanced Heat Map and Clustering Analysis Using Heatmap3

Heat maps and clustering are used frequently in expression analysis studies for data visualization and quality control. Simple clustering and heat maps can be produced from the heatmap function in R. However, the heatmap function lacks certain functionalities and customizability, preventing it from generating advanced heat maps and dendrograms. To tackle the limitations of the heatmap function, we have developed an R package heatmap3 which significantly improves the original heatmap function by adding several more powerful and convenient features. The heatmap3 package allows users to produce highly customizable state of the art heat maps and dendrograms. The heatmap3 package is developed based on the heatmap function in R, and it is completely compatible with it. The new features of heatmap3 include highly customizable legends and side annotation, a wider range of color selections, new labeling features which allow users to define multiple layers of phenotype variables, and automatically conducted association tests based on the phenotypes provided. Additional features such as different agglomeration methods for estimating distance between two samples are also added for clustering.